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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ), 'gf_id' => 'HOM05D001208', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001208' ), 'data_identifier' => 'HOM05D001208', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001208', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p32280' => 'bna', 'A04p04630' => 'bna', 'A04p04650' => 'bna', 'A06p33550' => 'bna', 'A07p03090' => 'bna', 'A08p01850' => 'bna', 'A09p12550' => 'bna', 'A09p48200' => 'bna', 'Aa31LG10G10150' => 'aar', 'Aa31LG10G10190' => 'aar', 'Aa31LG10G10200' => 'aar', 'Aa31LG10G10210' => 'aar', 'Aa31LG10G10220' => 'aar', 'Aa31LG10G10230' => 'aar', 'Aa31LG10G10240' => 'aar', 'Aa31LG10G10290' => 'aar', 'Aa31LG10G10320' => 'aar', 'Aa31LG5G11100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3853' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3858' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1155' => 'aag', 'Actinidia17962' => 'ach', 'Actinidia36213' => 'ach', 'Actinidia37876' => 'ach', 'Ah.02g119870' => 'amhyb', 'Ah.13g077100' => 'amhyb', 'Ah.16g108240' => 'amhyb', 'AL2G13260' => 'aly', 'AL3G10110' => 'aly', 'AL3G50880' => 'aly', 'AL5G36430' => 'aly', 'Aqoxy1G00168' => 'aox', 'Aqoxy1G00169' => 'aox', 'Aqoxy2G01367' => 'aox', 'Aqoxy5G03299' => 'aox', 'Aqoxy5G03300' => 'aox', 'arahy.Tifrunner.gnm1.ann1.ATUJ9U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DBA5QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EKF4XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G86GHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ICU8XT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KNM3C9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M30KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VC16G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W0JRJP' => 'arhy', 'AT1G62610' => 'ath', 'AT1G63380' => 'ath', 'AT2G17845' => 'ath', 'AT3G01980' => 'ath', 'AT3G46170' => 'ath', 'AT3G55290' => 'ath', 'AT3G55310' => 'ath', 'ATR0561G256' => 'atr', 'ATR0605G193' => 'atr', 'ATR0605G359' => 'atr', 'Atru.chr1.1407' => 'acertr', 'Atru.chr1.2714' => 'acertr', 'Atru.chr1.2716' => 'acertr', 'Atru.chr11.1128' => 'acertr', 'Atru.chr12.1000' => 'acertr', 'Atru.chr4.12' => 'acertr', 'Atru.chr6.2591' => 'acertr', 'AUR62003424' => 'cqu', 'AUR62018360' => 'cqu', 'AUR62029417' => 'cqu', 'AUR62030303' => 'cqu', 'AUR62037370' => 'cqu', 'BcaB01g00115' => 'bca', 'BcaB02g08431' => 'bca', 'BcaB02g08432' => 'bca', 'BcaB03g16559' => 'bca', 'BcaB04g17124' => 'bca', 'BcaC01g01355' => 'bca', 'BcaC01g02879' => 'bca', 'BcaC01g02882' => 'bca', 'BcaC02g09742' => 'bca', 'BcaC02g09743' => 'bca', 'BcaC05g26457' => 'bca', 'BcaC06g36336' => 'bca', 'BcaC07g39847' => 'bca', 'BolC1t02724H' => 'bol', 'BolC3t18135H' => 'bol', 'BolC3t18141H' => 'bol', 'BolC4t25277H' => 'bol', 'BolC4t25278H' => 'bol', 'BolC5t31233H' => 'bol', 'BolC7t40922H' => 'bol', 'BolC7t46139H' => 'bol', 'BraA03t12398Z' => 'bra', 'BraA04t16173Z' => 'bra', 'BraA04t16174Z' => 'bra', 'BraA04t16175Z' => 'bra', 'BraA04t16177Z' => 'bra', 'BraA04t16178Z' => 'bra', 'BraA06t26287Z' => 'bra', 'BraA06t26292Z' => 'bra', 'BraA07t28106Z' => 'bra', 'BraA08t32237Z' => 'bra', 'BraA09t36901Z' => 'bra', 'C01p02350' => 'bna', 'C01p23840' => 'bna', 'C02p06010' => 'bna', 'C03p23910' => 'bna', 'C03p58790' => 'bna', 'C03p90990' => 'bna', 'C04p37110' => 'bna', 'C04p37120' => 'bna', 'C04p37130' => 'bna', 'C05p25010' => 'bna', 'C07p05240' => 'bna', 'CAN.G107.31' => 'can', 'CAN.G128.82' => 'can', 'CAN.G128.83' => 'can', 'CAN.G1397.5' => 'can', 'CAN.G243.6' => 'can', 'CAN.G575.19' => 'can', 'CAN.G575.20' => 'can', 'CAN.G575.22' => 'can', 'CAN.G575.25' => 'can', 'CAN.G575.40' => 'can', 'CAN.G69.22' => 'can', 'CAN.G960.67' => 'can', 'CANSAT25G0719' => 'cansat', 'CANSAT64G1291' => 'cansat', 'CANSAT64G2207' => 'cansat', 'CARHR060750' => 'chi', 'CARHR074980' => 'chi', 'CARHR165290' => 'chi', 'CARHR220170' => 'chi', 'Carub.0002s0235' => 'cru', 'Carub.0002s0237' => 'cru', 'Carub.0002s0238' => 'cru', 'Carub.0003s0011' => 'cru', 'Carub.0003s3199' => 'cru', 'Carub.0005s2195' => 'cru', 'Ca_12781_v3' => 'car', 'Ca_20853_v3' => 'car', 'Ca_27713_v3' => 'car', 'Cc00_g19710' => 'ccan', 'Cc00_g27860' => 'ccan', 'Cc06_g19890' => 'ccan', 'Cc06_g19900' => 'ccan', 'Cc06_g19910' => 'ccan', 'Cc06_g19920' => 'ccan', 'Cc06_g21010' => 'ccan', 'Cc07_g00990' => 'ccan', 'CDE02G1210' => 'cde', 'CDE05G1947' => 'cde', 'CDE07G1682' => 'cde', 'CDE08G1580' => 'cde', 'Cfa007210' => 'cfa', 'Cfa016783' => 'cfa', 'Cfa016785' => 'cfa', 'Cfa027186' => 'cfa', 'Ciclev10012408m.g' => 'ccl', 'Ciclev10012421m.g' => 'ccl', 'Ciclev10012432m.g' => 'ccl', 'Ciclev10016277m.g' => 'ccl', 'CiPaw.04G039200' => 'cil', 'CiPaw.10G041400' => 'cil', 'CiPaw.10G041500' => 'cil', 'CiPaw.10G041600' => 'cil', 'CiPaw.10G041700' => 'cil', 'CiPaw.10G041800' => 'cil', 'ClCG00G005750' => 'cla', 'ClCG04G005730' => 'cla', 'ClCG05G013650' => 'cla', 'ClCG05G013660' => 'cla', 'ClCG08G002680' => 'cla', 'ClCG08G002690' => 'cla', 'ClCG08G003210' => 'cla', 'ClCG08G003220' => 'cla', 'ClCG10G003150' => 'cla', 'ClCG10G003170' => 'cla', 'ClCG10G015330' => 'cla', 'COL.COLO4_13288' => 'col', 'COL.COLO4_24748' => 'col', 'Cpa.g.sc70.122' => 'cpa', 'Cpa.g.sc92.85' => 'cpa', 'Cpa.g.sc92.95' => 'cpa', 'CsaV3_3G026900' => 'csa', 'CsaV3_3G041170' => 'csa', 'CsaV3_4G029410' => 'csa', 'CsaV3_4G029420' => 'csa', 'CsaV3_4G029440' => 'csa', 'CSS0020948' => 'camsi', 'CSS0034621' => 'camsi', 'CSS0037698' => 'camsi', 'DCAR_005182' => 'dca', 'DCAR_005183' => 'dca', 'DCAR_009934' => 'dca', 'DCAR_013648' => 'dca', 'DCAR_016885' => 'dca', 'DCAR_020583' => 'dca', 'DCAR_020584' => 'dca', 'DCAR_021803' => 'dca', 'DCAR_029594' => 'dca', 'DCAR_029623' => 'dca', 'DCAR_029624' => 'dca', 'DCAR_029625' => 'dca', 'Dinv05640' => 'din', 'Dinv05643' => 'din', 'Dinv05645' => 'din', 'Dinv05649' => 'din', 'Dinv21474' => 'din', 'Dinv25650' => 'din', 'Duzib128G0946' => 'dzi', 'Duzib147G0492' => 'dzi', 'Duzib264G1149' => 'dzi', 'ECA238G0379' => 'eca', 'ECA248G1111' => 'eca', 'ECA248G1442' => 'eca', 'ECA248G3741' => 'eca', 'EL10Ac3g07251' => 'bvu', 'EL10Ac6g15435' => 'bvu', 'Eucgr.A02228' => 'egr', 'Eucgr.I01632' => 'egr', 'FAN02G0417' => 'fan', 'FAN05G5470' => 'fan', 'FAN08G2391' => 'fan', 'FAN09G2806' => 'fan', 'FAN13G2922' => 'fan', 'FAN14G4456' => 'fan', 'FAN18G0917' => 'fan', 'FvH4_5g32470' => 'fve', 'FvH4_6g53780' => 'fve', 'Glyma.02G157200' => 'gma', 'Glyma.02G159200' => 'gma', 'Glyma.17G107900' => 'gma', 'Gohir.A05G039000' => 'ghi', 'Gohir.A05G336900' => 'ghi', 'Gohir.A07G230100' => 'ghi', 'Gohir.A09G036500' => 'ghi', 'Gohir.D04G075500' => 'ghi', 'Gohir.D05G040500' => 'ghi', 'Gohir.D07G237300' => 'ghi', 'Gohir.D09G037500' => 'ghi', 'Gorai.001G273200' => 'gra', 'Gorai.006G042900' => 'gra', 'Gorai.009G041000' => 'gra', 'Gorai.012G085000' => 'gra', 'GSVIVG01025751001' => 'vvi', 'GSVIVG01025752001' => 'vvi', 'GSVIVG01025755001' => 'vvi', 'GSVIVG01033062001' => 'vvi', 'HanXRQChr01g0007591' => 'han', 'HanXRQChr01g0008551' => 'han', 'HanXRQChr01g0008561' => 'han', 'HanXRQChr01g0008571' => 'han', 'HanXRQChr01g0008591' => 'han', 'HanXRQChr01g0008601' => 'han', 'HanXRQChr02g0048931' => 'han', 'HanXRQChr05g0132051' => 'han', 'HanXRQChr05g0132061' => 'han', 'HanXRQChr05g0132071' => 'han', 'HanXRQChr07g0198141' => 'han', 'HanXRQChr10g0292401' => 'han', 'HanXRQChr10g0317151' => 'han', 'HanXRQChr13g0387781' => 'han', 'HanXRQChr13g0387791' => 'han', 'Haze_14894' => 'cav', 'Haze_19801' => 'cav', 'Haze_20245' => 'cav', 'Hma1.2p1_0455F.1_g156320' => 'hma', 'Hma1.2p1_1057F.1_g252710' => 'hma', 'HPP92_000458' => 'vpl', 'HPP92_000464' => 'vpl', 'HPP92_016026' => 'vpl', 'HPP92_023386' => 'vpl', 'HPP92_024288' => 'vpl', 'HPP92_024310' => 'vpl', 'Hund07876' => 'sun', 'Hund19083' => 'sun', 'Hund24568' => 'sun', 'Hund24569' => 'sun', 'Lalb_Chr01g0012801' => 'lal', 'Lalb_Chr01g0012901' => 'lal', 'Lalb_Chr02g0156631' => 'lal', 'Lalb_Chr21g0316731' => 'lal', 'Lalb_Chr21g0316741' => 'lal', 'Lalb_Chr21g0316751' => 'lal', 'Lalb_Chr21g0316761' => 'lal', 'Lalb_Chr21g0316771' => 'lal', 'Lalb_Chr21g0316781' => 'lal', 'Lalb_Chr25g0281101' => 'lal', 'Lalb_Chr25g0281111' => 'lal', 'Lj1C1087G5' => 'lonja', 'Lj1C1087T6' => 'lonja', 'Lj1C1088G6' => 'lonja', 'Lj1g0008529' => 'lja', 'Lj1g0009675' => 'lja', 'Lj1g0011329' => 'lja', 'Lj1g0026775' => 'lja', 'Lj2A402G42' => 'lonja', 'Lj2A403G31' => 'lonja', 'Lju41C54T2' => 'lonja', 'Lsat_1_v5_gn_2_94301' => 'lsa', 'Lsat_1_v5_gn_3_134240' => 'lsa', 'Lsat_1_v5_gn_4_40481' => 'lsa', 'Lsat_1_v5_gn_5_156441' => 'lsa', 'Lsat_1_v5_gn_5_156481' => 'lsa', 'Lsat_1_v5_gn_7_91101' => 'lsa', 'Lsat_1_v5_gn_7_91121' => 'lsa', 'Lsat_1_v5_gn_8_74420' => 'lsa', 'Lsat_1_v5_gn_8_79680' => 'lsa', 'Manes.08G060801' => 'mes', 'Manes.15G162700' => 'mes', 'Mapoly0081s0082' => 'mpo', 'Mapoly0095s0044' => 'mpo', 'MBI01_g20388_MAGBIO' => 'mbi', 'MBI01_g20623_MAGBIO' => 'mbi', 'MBI01_g36101_MAGBIO' => 'mbi', 'MBI04_g21999_MAGBIO' => 'mbi', 'MBI11_g05338_MAGBIO' => 'mbi', 'MD09G1008700' => 'mdo', 'MD12G1006600' => 'mdo', 'MD12G1094700' => 'mdo', 'MD15G1420800' => 'mdo', 'MD15G1420900' => 'mdo', 'MD17G1001600' => 'mdo', 'Medtr1g007800' => 'mtr', 'Medtr1g051165' => 'mtr', 'Medtr4g058810' => 'mtr', 'Medtr4g058820' => 'mtr', 'Medtr4g058830' => 'mtr', 'Medtr4g058840' => 'mtr', 'MELO3C009846.2' => 'cme', 'MELO3C014897.2' => 'cme', 'MELO3C015036.2' => 'cme', 'MELO3C019108.2' => 'cme', 'MELO3C019109.2' => 'cme', 'Migut.J01638' => 'egut', 'Migut.K00142' => 'egut', 'Migut.K00143' => 'egut', 'Migut.K00144' => 'egut', 'Migut.K00145' => 'egut', 'Migut.K01476' => 'egut', 'MSTRG.26164' => 'ama', 'MSTRG.26166' => 'ama', 'MSTRG.3068' => 'ama', 'MSTRG.5999' => 'ama', 'MSTRG.6344' => 'ama', 'Nitab4.5_0000062g0120' => 'nta', 'Nitab4.5_0000189g0050' => 'nta', 'Nitab4.5_0000189g0080' => 'nta', 'Nitab4.5_0000441g0030' => 'nta', 'Nitab4.5_0000812g0020' => 'nta', 'Nitab4.5_0001384g0030' => 'nta', 'Nitab4.5_0001384g0040' => 'nta', 'Nitab4.5_0001384g0070' => 'nta', 'Nitab4.5_0002479g0020' => 'nta', 'Nitab4.5_0005192g0010' => 'nta', 'Nitab4.5_0007633g0010' => 'nta', 'Nitab4.5_0010244g0020' => 'nta', 'Nitab4.5_0012159g0010' => 'nta', 'Nn2g15644' => 'nnu', 'Nn2g15645' => 'nnu', 'Nn4g22263' => 'nnu', 'Nn7g36028' => 'nnu', 'Oeu027948.1' => 'oeu', 'Oeu048915.2' => 'oeu', 'Os03g0850000' => 'osa', 'Os08g0510400' => 'osa', 'Peaxi162Scf00003g05029' => 'pax', 'Peaxi162Scf00010g00153' => 'pax', 'Peaxi162Scf00010g00177' => 'pax', 'Peaxi162Scf00010g00181' => 'pax', 'Peaxi162Scf00010g01318' => 'pax', 'Peaxi162Scf00010g01615' => 'pax', 'Peaxi162Scf00010g01910' => 'pax', 'Peaxi162Scf00062g01316' => 'pax', 'Peaxi162Scf00083g00619' => 'pax', 'Peaxi162Scf00160g01753' => 'pax', 'Peaxi162Scf00776g00122' => 'pax', 'Peaxi162Scf00811g00011' => 'pax', 'Peaxi162Scf01320g00002' => 'pax', 'PGR042G0631' => 'pgr', 'PGR042G2842' => 'pgr', 'PGR042G3276' => 'pgr', 'PGR142G2960' => 'pgr', 'PGSC0003DMG400005592' => 'stu', 'PGSC0003DMG400007169' => 'stu', 'PGSC0003DMG400008363' => 'stu', 'PGSC0003DMG400008364' => 'stu', 'PGSC0003DMG400011601' => 'stu', 'PGSC0003DMG400011602' => 'stu', 'PGSC0003DMG400014094' => 'stu', 'PGSC0003DMG400014095' => 'stu', 'PGSC0003DMG400023847' => 'stu', 'PGSC0003DMG400024450' => 'stu', 'PGSC0003DMG400025005' => 'stu', 'PGSC0003DMG400028097' => 'stu', 'PGSC0003DMG400033642' => 'stu', 'PGSC0003DMG400037729' => 'stu', 'PGSC0003DMG400042005' => 'stu', 'PGSC0003DMG400046107' => 'stu', 'PGSC0003DMG402006147' => 'stu', 'Phvul.003G171900' => 'pvu', 'Phvul.007G242800' => 'pvu', 'Phvul.007G242900' => 'pvu', 'Potri.001G327800' => 'ptr', 'Potri.016G035200' => 'ptr', 'Potri.017G067332' => 'ptr', 'Pp3c13_10810' => 'ppa', 'Pp3c20_20520' => 'ppa', 'Pp3c3_8860' => 'ppa', 'Prupe.3G308300' => 'ppe', 'Prupe.7G031300' => 'ppe', 'Psat6g035480' => 'psa', 'Psat6g128640' => 'psa', 'Psat7g144600' => 'psa', 'Psat7g144640' => 'psa', 'Psat7g144680' => 'psa', 'PSO017G3242' => 'pso', 'PSO478G2417' => 'pso', 'PSO500G0273' => 'pso', 'PSO675G3462' => 'pso', 'QL02p070951' => 'qlo', 'QL02p070962' => 'qlo', 'QL07p011572' => 'qlo', 'QL07p011636' => 'qlo', 'QL07p011654' => 'qlo', 'QL07p011686' => 'qlo', 'QL07p011698' => 'qlo', 'RcHm_v2.0_Chr2g0175921' => 'rch', 'RcHm_v2.0_Chr7g0229021' => 'rch', 'RcHm_v2.0_Chr7g0229051' => 'rch', 'RcHm_v2.0_Chr7g0229061' => 'rch', 'Rhsim03G0036000' => 'rsi', 'Rhsim03G0036100' => 'rsi', 'Rhsim03G0036200' => 'rsi', 'Rhsim03G0036300' => 'rsi', 'Rhsim10G0005000' => 'rsi', 'Sabra06G0025000' => 'sbr', 'Sabra16G0037500' => 'sbr', 'Sabra17G0058700' => 'sbr', 'SalBow1G0874' => 'sbo', 'SalBow1G3660' => 'sbo', 'SalBow1G3719' => 'sbo', 'SalBow1G5321' => 'sbo', 'SalBow1G6352' => 'sbo', 'SalBow6G2971' => 'sbo', 'SalBow7G1798' => 'sbo', 'Sc08g0005580' => 'sci', 'Sc13g0001020' => 'sci', 'Sed0003618' => 'sed', 'Sed0006182' => 'sed', 'Sed0013841' => 'sed', 'Sed0020213' => 'sed', 'Sed0025366' => 'sed', 'SEGI_02921' => 'sgi', 'SEGI_16400' => 'sgi', 'SEGI_30001' => 'sgi', 'SGA_v2.0_scaffold106G30529' => 'sas', 'SGA_v2.0_scaffold44G16927' => 'sas', 'SMO172G0163' => 'smo', 'SMO358G0557' => 'smo', 'SMO358G0758' => 'smo', 'Solyc07g047800.3' => 'sly', 'Solyc10g006860.4' => 'sly', 'Solyc10g078360.3' => 'sly', 'Solyc10g080890.2' => 'sly', 'Solyc10g080900.3' => 'sly', 'Solyc12g036510.1' => 'sly', 'Solyc12g044940.2' => 'sly', 'Solyc12g045030.2' => 'sly', 'Solyc12g100220.2' => 'sly', 'Solyc12g100280.3' => 'sly', 'Sopen01g006110' => 'spe', 'Sopen07g024240' => 'spe', 'Sopen10g002770' => 'spe', 'Sopen10g029020' => 'spe', 'Sopen10g031400' => 'spe', 'Sopen10g031410' => 'spe', 'Sopen12g023300' => 'spe', 'Sopen12g023390' => 'spe', 'Sopen12g023400' => 'spe', 'Sopen12g034900' => 'spe', 'Sp3g00130' => 'spa', 'Sp3g31300' => 'spa', 'Sp5g07170' => 'spa', 'Sp5g07175' => 'spa', 'TAR012G0001' => 'tar', 'TAR369G0941' => 'tar', 'TAR491G0002' => 'tar', 'TAR622G0816' => 'tar', 'TAR626G1303' => 'tar', 'TAR626G1766' => 'tar', 'TAR629G0484' => 'tar', 'TAR633G1646' => 'tar', 'THA.LOC104806573' => 'tha', 'THA.LOC104821132' => 'tha', 'Thecc.04G039800' => 'tca', 'Thecc.05G124700' => 'tca', 'Thhalv10002227m.g' => 'esa', 'Thhalv10010605m.g' => 'esa', 'Thhalv10010610m.g' => 'esa', 'Thhalv10021329m.g' => 'esa', 'TPR.G13794' => 'tpr', 'TPR.G22108' => 'tpr', 'TPR.G24529' => 'tpr', 'TPR.G40126' => 'tpr', 'TWI32G0053' => 'twi', 'TWI53G1705' => 'twi', 'TWI77G0504' => 'twi', 'unitig_0.g2665' => 'ugi', 'unitig_0.g2666' => 'ugi', 'unitig_46.g18437' => 'ugi', 'unitig_748.g7134' => 'ugi', 'vmacro05971' => 'vma', 'vmacro07775' => 'vma', 'vmacro07776' => 'vma', 'VMungo0720G0076' => 'vmu', 'VMungo0720G2329' => 'vmu', 'VMungo1215G3005' => 'vmu', 'Zm00001eb035040' => 'zma', 'Zm00001eb210770' => 'zma' ) $gf_id = 'HOM05D001208' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001208' ) $data_identifier = 'HOM05D001208' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 10, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 9, 'ath' => (int) 7, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 11, 'can' => (int) 12, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 6, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 11, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 3, 'dca' => (int) 12, 'din' => (int) 6, 'dzi' => (int) 3, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 15, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 9, 'mes' => (int) 2, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 13, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 2, 'pax' => (int) 13, 'pgr' => (int) 4, 'stu' => (int) 17, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 7, 'sci' => (int) 2, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 10, 'spe' => (int) 10, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb210770' $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